Actually, it is probably more my area to answer this. Inline replies. Tim
On Fri, Jun 14, 2013 at 1:40 PM, Colin Reveley <cm...@sussex.ac.uk> wrote: > Hi - I guess this is a question specificially for matt. > > I have some FSL processed diffusion data. I want to display the mean fibre > orientations in "little colored lines on top of a volume" format. > > fslview does this. it's very common. the problem is that the data is very > high resolution. So you really can't see the little lines if you print the > image from FSLview. > > One way around this is caret_command -volume-fsl-to-vector > > I accept this is unsupported. but it does provide a better display for my > needs in that the way the vectors appear on the screen is more configurable > and generally makes a better figure. > > only: > > that command works and thinks in terms of axial slices and the display is > interms of distances above and below the axial plane. > > this means that in coronal view it can end up looking a bit off. > > I was wondering: > > surely workbench now has a neat-o way of displaying fibers? > > it looks like it does. > > but how to get the data in there? > > there is > > wb_command -estimate-fiber-binghams > and > wb_command -convert-fiber-orientations > -estimate-fiber-binghams is probably what you want, -convert-fiber-orientations is for when diffusion processing estimates binghams directly, which I'm not sure is released yet. > > since bedpostx does not output ka or kb (or std_dev normally, maybe it > does in some circumstances) I presume the former command serves as input to > the latter in some way > No, they have the same kind of output, but different input. > how exactly would that work, to create a nice volume display of fibers in > workbench? in particualar, the input to -est-fib-bing requires a label > volume. is this a volume of integers? where is the specification of what > the CIFTI idenifiers (eg CORTEX RIGHT) actually map to as numbers? > There are no fixed numbers, it uses the strings, you just have to generate a workbench style label volume with those strings as the label names. However, there are fixed numbers for the freesurfer parcellations of the corresponding structures, and matt may be able to help you there. Alternatively, you can just take a white matter segmentation volume and assign something appropriate to the "true" value (usually 1). > generally, is it possible to make a fiber file for display in WB given > suitable data, and e.g. a FAST segmantation relabelled to the CIFTI > itentifier values? > Strings, not values, and yes, it doesn't care where it comes from, it just has to match the volume space of the fiber data. > Given my goals as described above, do I even want to be trying this? > I don't see why not. There are a few options in fiber display in workbench, and the fibers are in free space, rather than realigned to voxel centers, which sounds like a problem you were having.
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